[Biojava-l] Rooted trees in nexus files

[Tiago Antão]

If somebody would provide the desired changes to the parser interface
(wrt this bug and the other one reported previously), I might offer to
to the grunt work.

But somebody has to say which interface changes are desired.
I remember which problems exist:
1. Lack of knowledge of root node
2. The p* stuff.

Tiago
2009/11/3 Richard Holland <holland at eaglegenomics.com>:
> Agreed that there is a bug. Now all we need is someone to go in and fix it!
> :)
>
> cheers,
> Richard
>
> On 3 Nov 2009, at 18:16, Tiago Antão wrote:
>
>> 2009/11/3 Thasso Griebel <thasso.griebel at uni-jena.de>:
>>>
>>> There is a way to uniquely  get a root from a newick string. Usually a
>>> rooted newick is surrounded with brackets, which indicates the root as
>>> the
>>> highest node in the tree. For example:
>>>
>>> (A, (B,C))
>>>
>>
>> Agree, it is quite easy to get the root of the tree from the newick
>> representation. But it should be done on parsing and returned in some
>> way by the parsing system. If the user has to do it again, it means
>> that the user has to parse it again just to know the root node.
>>
>>> I would also suggest to generally parse trees as rooted trees (maybe jsut
>>> for th initial internal model). Creating an unrooted tree from a rooted
>>>  one
>>> is easy, remove the root and forget about directions. The other way might
>>> be
>>> hard and ambiguous.
>>
>> 100% agree.
>> The newick _representation_ always has a root by virtue of the way it
>> is done. If that root has meaning or not depends. Doing as you suggest
>> seems the most reasonable idea.
>> I would add that even if it is an unrooted tree, the topology might be
>> of interest. In my case I am doing a comparative visualizer and it
>> might be nice for the user to be able to visualize the topology as
>> specified. It has no biological meaning, but in practice, for many
>> users, it helps.
>> I note that PhyloXML (even by virtue of being a XML format) always
>> represents the phylogenies as trees (not weigthed DAGs). There an
>> attribute rooted which can be true or false.
>>
>> But, anyway. Even assuming a very conservative view on this, the
>> current parser, for rooted trees, does not allow to determine where is
>> the root. I think that there would be a consensus that that is a bug?
>>
>> Tiago
>
> --
> Richard Holland, BSc MBCS
> Operations and Delivery Director, Eagle Genomics Ltd
> T: +44 (0)1223 654481 ext 3 | E: holland at eaglegenomics.com
> http://www.eaglegenomics.com/
>
>



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